3NN3

Structure of chlorite dismutase from Candidatus Nitrospira defluvii R173A mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIN-HOUSE MODEL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62951.4M ammonium phosphate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.0659.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.74α = 90
b = 113.62β = 118.94
c = 120.52γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42009-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.6105.492.150785
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.62.6779.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTIN-HOUSE MODEL2.644.394816748167257799.90.21420.21420.2120.25434RANDOM73.031
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.34-4.3-1.83-2.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.763
r_dihedral_angle_4_deg18.566
r_dihedral_angle_3_deg16.864
r_dihedral_angle_1_deg5.612
r_scangle_it1.769
r_angle_refined_deg1.243
r_scbond_it1.221
r_angle_other_deg0.881
r_mcangle_it0.721
r_mcbond_it0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.763
r_dihedral_angle_4_deg18.566
r_dihedral_angle_3_deg16.864
r_dihedral_angle_1_deg5.612
r_scangle_it1.769
r_angle_refined_deg1.243
r_scbond_it1.221
r_angle_other_deg0.881
r_mcangle_it0.721
r_mcbond_it0.61
r_symmetry_hbond_refined0.232
r_nbd_refined0.209
r_nbd_other0.187
r_symmetry_vdw_refined0.186
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.178
r_symmetry_vdw_other0.17
r_mcbond_other0.151
r_nbtor_other0.086
r_chiral_restr0.067
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9565
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms315

Software

Software
Software NamePurpose
DNAdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling